Re: [Gusdev-rad-issues] question on arrayresultloader plugin

[Junmin L. <ju...@pc...>]

This plugin doesn't support loading elementResult for affy data. It only 
load compositeElementResult for affy data. I think it is current way we 
use RAD in cbil.
--junmin


On Wed, 14 Dec 2005, Elisabetta Manduchi wrote:

>
> Hi Sucheta,
> the first thing you need to check is that you are complying with the 
> documentation for this plugin, especially in the input data_file format.
> HTML documentation can be generated by running the plugin with just the 
> --helpHTML option.
> If you are using GUS 3.5 this plugin is named LoadArrayResults and 
> documentation is also available at 
> https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/doc/LoadArrayResults.html
> The usage of this plugin didn't change much from 3.0 to 3.5.
>
> Now, it looks like you are trying to simultaenously load both the .CEL and 
> the MAS 5 probe set results. I'm not sure the plugin can handle this, that 
> is, you might need to load separately the results for the CEL and the MAS 5 
> probeset quantifications (note that they should refer to different 
> quantifications). But I'll let JUNMIN  (here cc-ed) confirm on this, as he is 
> the author of this plugin. I see that the plugin documentation is not clear 
> on this point. Here we typically load only the probe_set results in the db 
> (e.g. AffymetrixMAS4 or AffymetrixMAS5 or RMAExpress views). For the .cel 
> files we simply create a quantification in RAD.Quantification for the .cel 
> results with the uri pointing to where we hold the .CEL  file in our 
> filesystem.
> If loading only the probeset results, the typical header of the data_file 
> should be:
> name	signal	detection	detection_p_value
>
> (and optionally also stat_pairs and stat_pairs_used)
> tab separated, no commas.
>
> In any case, should you still have problems after checking the data format, 
> please email Junmin directly. Make sure you include in your email: GUS 
> version you are using, command line, top portion of the data_file, any error 
> message you get, and description of the problem
>
> Elisabetta
> P.S. Note that we also have a batch result loader that works for MAS5 probe 
> set results loading them in batch. In GUS 3.5 the name of this
> plugin is GUS::Community::Plugin::LoadBatchArrayResults.
>
> ---
>
> On Wed, 14 Dec 2005, Sucheta Tripathy wrote:
>
>> Hi Elisabetta,
>> 
>> I am using arrayresultloader to upload the array data into GUS. It does a 
>> decent job but crashes inbetween without giving a proper error message. 
>> Could it be due to my computer related issues.
>> 
>> Also when I have a line having data such as:
>> 
>> x_position, y_position, mean,       stdv,       npixels,       name, 
>> detection,      detection_p_value,    signal
>> 621            275           76.0           10.5       25 
>> PsAffx.C17000127_at   A                 0.111572                  10.95974
>> 
>> But when I upload the data it changes the fields into:
>> 
>> Debug   621    275    44.0    7.5    25    PsAffx.C17000127_at       A 0.24
>> 6094      10.821429
>> 
>> and says mean 44.0 and stdv 7.5 etc.
>> 
>> Is there a reason why the values are changed?
>> 
>> Thanks
>> 
>> Sucheta
>> 
>> 
>> 
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>
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